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Average Coverage after Assembly (Spades)
Hi, I would like to know to average coverage of my assemblies (gotten by spades). I ran bbmap to mapping my reads (the same ones I used to make the assembly) to the assembly. But I am not really sure that is the way and the answers on the different forums didn't completely help.
Command
bbmap.sh in=./trimmed/NM167_S34_R1.fastq in2=./trimmed/NM167_S34_R2.fastq ref=./assembly/NM167_S34.fasta covstats=covstats.txt
I got output like this:
#ID Avg_fold Length Ref_GC Covered_percent Covered_bases Plus_reads Minus_reads Read_GC Median_fold Std_Dev
NODE_1_length_79421_cov_85.482448 261.1709 79421 0.5185 100.0000 79421 60378 60230 0.5259 253 111.34
....
I will really appreciate your help!
Thank you
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2 answers
Hi,
I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
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bbmap.sh in=./trimmed/NM167_S34_R1.fastq in2=./trimmed/NM167_S34_R2.fastq ref=./assembly/NM167_S34.fasta covstats=covstats.txt 1>screen.txt 2>&1
...will redirect the screen output. The screen output goes to stderr (2>) not stdout (1>).
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I see now I got the average, but it's printed on the terminal and doesn't appear in the covstats.txt file
Average coverage: 164.398 Standard deviation: 155.626 Percent scaffolds with any coverage: 84.91 Percent of reference bases covered: 99.56
And I don't know how to set it in a file I tried with the redirect output ">" but it is not working
Any Idea ?
Thank you